4-160870229-G-C

Variant names:

• chr4-160870229-G-C
• rs6811083

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.331 in 151,964 control chromosomes in the GnomAD database, including 11,418 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.33 (11418 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.408
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.637 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.331 AC: 50241 AN: 151846 Hom.: 11386 Cov.: 32

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.322

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.331 AC: 50328 AN: 151964 Hom.: 11418 Cov.: 32 AF XY: 0.321 AC XY: 23862 AN XY: 74256

African (AFR) AF: 0.644 AC: 26692 AN: 41454

American (AMR) AF: 0.221 AC: 3376 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 944 AN: 3470

East Asian (EAS) AF: 0.148 AC: 763 AN: 5162

South Asian (SAS) AF: 0.269 AC: 1294 AN: 4810

European-Finnish (FIN) AF: 0.104 AC: 1097 AN: 10544

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.223 AC: 15127 AN: 67948

Other (OTH) AF: 0.323 AC: 681 AN: 2108

Alfa AF: 0.105 Hom.: 141

Bravo AF: 0.354

Asia WGS AF: 0.222 AC: 770 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.5
DANN	Benign	0.32
PhyloP100		0.41

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6811083; hg19: chr4-161791381;